Merge branch 'plugin/schisto' into plugin-conda-deps

.github/workflows/build-and-test.yml

@@ -28,10 +28,10 @@ jobs:
     name: Check for syntax errors
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ env.LATEST_SUPPORTED_PYTHON_VERSION }}
 
@@ -46,13 +46,13 @@ jobs:
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
           python -m flake8 src --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
 
-  check-history-rst-syntax:
-    name: Check HISTORY RST syntax
+  check-rst-syntax:
+    name: Check RST syntax
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Set up python
         with:
           python-version: ${{ env.LATEST_SUPPORTED_PYTHON_VERSION }}
@@ -63,7 +63,7 @@ jobs:
       - name: Lint with doc8
         run: |
             # Skip line-too-long errors (D001)
-            python -m doc8 --ignore D001 HISTORY.rst
+            python -m doc8 --ignore D001 HISTORY.rst README_PYTHON.rst
 
   run-model-tests:
     name: Run model tests
@@ -75,7 +75,7 @@ jobs:
         python-version: [3.8, 3.9, "3.10", "3.11", "3.12"]
         os: [windows-latest, macos-13]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch complete history for accurate versioning
 
@@ -127,27 +127,27 @@ jobs:
         run: make test
 
       - name: Upload wheel artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: Wheel for ${{ matrix.os }} ${{ matrix.python-version }}
           path: dist
 
       - name: Upload conda env artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         continue-on-error: true
         with:
           name: Conda Env for ${{ matrix.os }} ${{ matrix.python-version }}
           path: conda-env.txt
 
       - name: Authenticate GCP
         if: github.event_name != 'pull_request'
-        uses: google-github-actions/auth@v0
+        uses: google-github-actions/auth@v2
         with:
           credentials_json: ${{ secrets.GOOGLE_SERVICE_ACC_KEY }}
 
       - name: Set up GCP
         if: github.event_name != 'pull_request'
-        uses: google-github-actions/setup-gcloud@v0
+        uses: google-github-actions/setup-gcloud@v2
 
       - name: Deploy artifacts to GCS
         if: github.event_name != 'pull_request'
@@ -162,15 +162,15 @@ jobs:
         python-version: [3.8, 3.9, "3.10", "3.11", "3.12"]
         os: [windows-latest, macos-13]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0  # Fetch complete history for accurate versioning
 
       - uses: ./.github/actions/setup_env
         with:
           python-version: ${{ matrix.python-version }}
           requirements-files: requirements.txt
-          requirements: ${{ env.CONDA_DEFAULT_DEPENDENCIES }}
+          requirements: ${{ env.CONDA_DEFAULT_DEPENDENCIES }} twine
 
       - name: Build source distribution
         run: |
@@ -193,9 +193,12 @@ jobs:
           # natcap.invest from source and that it imports.
           python -c "from natcap.invest import *"
 
-      - uses: actions/upload-artifact@v3
+      - name: Check long description with twine
+        run: twine check $(find dist -name "natcap[._-]invest*")
+
+      - uses: actions/upload-artifact@v4
         with:
-          name: Source distribution
+          name: Source distribution ${{ matrix.os }} ${{ matrix.python-version }}
           path: dist
 
         # Secrets not available in PR so don't use GCP.
@@ -204,13 +207,13 @@ jobs:
         # different extensions)
       - name: Authenticate GCP
         if: github.event_name != 'pull_request' && matrix.os == 'macos-13' && matrix.python-version == env.LATEST_SUPPORTED_PYTHON_VERSION
-        uses: google-github-actions/auth@v0
+        uses: google-github-actions/auth@v2
         with:
           credentials_json: ${{ secrets.GOOGLE_SERVICE_ACC_KEY }}
 
       - name: Set up GCP
         if: github.event_name != 'pull_request' && matrix.os == 'macos-13' && matrix.python-version == env.LATEST_SUPPORTED_PYTHON_VERSION
-        uses: google-github-actions/setup-gcloud@v0
+        uses: google-github-actions/setup-gcloud@v2
 
       - name: Deploy artifacts to GCS
         if: github.event_name != 'pull_request' && matrix.os == 'macos-13' && matrix.python-version == env.LATEST_SUPPORTED_PYTHON_VERSION
@@ -221,7 +224,7 @@ jobs:
     runs-on: windows-latest
     needs: check-syntax-errors
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch complete history for accurate versioning
 
@@ -252,7 +255,7 @@ jobs:
 
     steps:
       - name: Check out repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch complete history for accurate versioning
 
@@ -309,7 +312,7 @@ jobs:
             workspace-path: ${{ github.workspace }}
             binary-extension: exe
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch complete history for accurate versioning
 
@@ -383,13 +386,13 @@ jobs:
 
       - name: Authenticate GCP
         if: github.event_name != 'pull_request'
-        uses: google-github-actions/auth@v0
+        uses: google-github-actions/auth@v2
         with:
           credentials_json: ${{ secrets.GOOGLE_SERVICE_ACC_KEY }}
 
       - name: Set up GCP
         if: github.event_name != 'pull_request'
-        uses: google-github-actions/setup-gcloud@v0
+        uses: google-github-actions/setup-gcloud@v2
 
       - name: Build Workbench (PRs)
         if: github.event_name == 'pull_request'
@@ -458,20 +461,20 @@ jobs:
 
       - name: Upload workbench binary artifact
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: Workbench-${{ runner.os }}-binary
           path: workbench/dist/*.${{ matrix.binary-extension }}
 
       - name: Upload user's guide artifact (Windows)
         if: matrix.os == 'windows-latest'
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: InVEST-user-guide
           path: dist/InVEST_*_userguide.zip
 
       - name: Upload workbench logging from puppeteer
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: always()
         with:
           name: ${{ runner.os }}_puppeteer_log.zip'
@@ -490,7 +493,7 @@ jobs:
 
       - name: Upload workspace on failure
         if: ${{ failure() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: InVEST-failed-${{ runner.os }}-workspace
           path: ${{ matrix.workspace-path}}
@@ -500,11 +503,11 @@ jobs:
     needs: check-syntax-errors
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch complete history for accurate versioning
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ env.LATEST_SUPPORTED_PYTHON_VERSION }}
 
@@ -515,20 +518,20 @@ jobs:
       - run: make sampledata sampledata_single
 
       - name: Upload sample data artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: InVEST-sample-data
           path: dist/*.zip
 
       - name: Authenticate GCP
         if: github.event_name != 'pull_request'
-        uses: google-github-actions/auth@v0
+        uses: google-github-actions/auth@v2
         with:
           credentials_json: ${{ secrets.GOOGLE_SERVICE_ACC_KEY }}
 
       - name: Set up GCP
         if: github.event_name != 'pull_request'
-        uses: google-github-actions/setup-gcloud@v0
+        uses: google-github-actions/setup-gcloud@v2
 
       - name: Deploy artifacts to GCS
         if: github.event_name != 'pull_request'

HISTORY.rst

@@ -37,8 +37,41 @@
 
 Unreleased Changes
 ------------------
+* General
+    * InVEST has been updated to build against numpy 2.
+      https://github.com/natcap/invest/issues/1641
+    * Updating validation to handle a change in exceptions raised by GDAL in
+      ``pygeoprocessing.get_raster_info`` and
+      ``pygeoprocessing.get_vector_info``.
+      https://github.com/natcap/invest/issues/1645
+* Forest Carbon Edge Effects
+    * Updating vector reprojection to allow partial reprojection.  Related to
+      https://github.com/natcap/invest/issues/1645
+* Urban Nature Access
+    * The model now works as expected when the user provides an LULC raster
+      that does not have a nodata value defined.
+      https://github.com/natcap/invest/issues/1293
 * Workbench
-  * Several small updates to the model input form UI to improve usability and visual consistency (https://github.com/natcap/invest/issues/912)
+    * Several small updates to the model input form UI to improve usability
+      and visual consistency (https://github.com/natcap/invest/issues/912).
+    * Fixed a bug that caused the application to crash when attempting to
+      open a workspace without a valid logfile
+      (https://github.com/natcap/invest/issues/1598).
+    * Fixed a bug that was allowing readonly workspace directories on Windows
+      (https://github.com/natcap/invest/issues/1599).
+    * Fixed a bug that, in certain scenarios, caused a datastack to be saved
+      with relative paths when the Relative Paths checkbox was left unchecked
+      (https://github.com/natcap/invest/issues/1609).
+    * Improved error handling when a datastack cannot be saved with relative
+      paths across drives (https://github.com/natcap/invest/issues/1608).
+* Habitat Quality
+    * Access raster is now generated from the reprojected access vector
+      (https://github.com/natcap/invest/issues/1615).
+    * Rarity values are now output in CSV format (as well as in raster format)
+      (https://github.com/natcap/invest/issues/721).
+* Urban Flood Risk
+    * Fields present on the input AOI vector are now retained in the output.
+      (https://github.com/natcap/invest/issues/1600)
 
 3.14.2 (2024-05-29)
 -------------------

Makefile

@@ -10,7 +10,7 @@ GIT_TEST_DATA_REPO_REV      := 324abde73e1d770ad75921466ecafd1ec6297752
 
 GIT_UG_REPO                 := https://github.com/natcap/invest.users-guide
 GIT_UG_REPO_PATH            := doc/users-guide
-GIT_UG_REPO_REV             := 0404bc5d4d43085cdc58f50f8fc29944b10cefb1
+GIT_UG_REPO_REV             := f203ec069f9f03560c9a85b268e67ebb6b994953
 
 ENV = "./env"
 ifeq ($(OS),Windows_NT)

constraints_tests.txt

@@ -6,5 +6,7 @@
 # occur with regular use of invest. https://github.com/OSGeo/gdal/issues/8497
 GDAL!=3.6.*,!=3.7.*
 
-# https://github.com/natcap/pygeoprocessing/issues/387
-GDAL<3.8.5
+# Pyinstaller 6.10 breaks our windows builds.  Until we can figure out the
+# root cause, let's cap the versions to those that work.
+# https://github.com/natcap/invest/issues/1622
+#pyinstaller<6.10

doc/api-docs/conf.py

@@ -78,13 +78,11 @@
 # -- Options for HTML output ----------------------------------------------
 
 import sphinx_rtd_theme
+
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 html_theme = 'sphinx_rtd_theme'
 
-# Add any paths that contain custom themes here, relative to this directory.
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
-
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
 html_logo = "_static/invest-logo.png"
@@ -130,16 +128,16 @@
 #  dir menu entry, description, category)
 texinfo_documents = [
   ('index', 'InVEST', 'InVEST Documentation',
-   'The Natural Capital Project', 'InVEST', 
+   'The Natural Capital Project', 'InVEST',
    'Integrated Valuation of Ecosystem Services and Tradeoffs',
    'Scientific Software'),
 ]
 
 
 # -- Prepare for sphinx build ---------------------------------------------
 
-# Use sphinx apidoc tool to generate documentation for invest. Generated rst 
-# files go into the api/ directory. Note that some apidoc options may not work 
+# Use sphinx apidoc tool to generate documentation for invest. Generated rst
+# files go into the api/ directory. Note that some apidoc options may not work
 # the same because we aren't using their values in the custom templates
 apidoc.main([
     '--force',  # overwrite any files from previous run
@@ -164,7 +162,7 @@
 
 All InVEST models share a consistent python API:
 
-    - Every InVEST model has a corresponding module or subpackage in the 
+    - Every InVEST model has a corresponding module or subpackage in the
       ``natcap.invest`` package
     - The model modules contain a function called ``execute``
     - The ``execute`` function takes a single argument (``args``), a dictionary

exe/hooks/rthook.py

@@ -1,9 +1,6 @@
-import sys
 import os
-import multiprocessing
 import platform
-
-multiprocessing.freeze_support()
+import sys
 
 os.environ['PROJ_LIB'] = os.path.join(sys._MEIPASS, 'proj')
 

exe/invest.spec

@@ -31,7 +31,9 @@ kwargs = {
         'pkg_resources.py2_warn',
         'cmath',
         'charset_normalizer',
-        'scipy.special._cdflib'
+        'scipy.special._cdflib',
+        'scipy.special._special_ufuncs',
+        'scipy._lib.array_api_compat.numpy.fft',
     ],
     'datas': [proj_datas],
     'cipher': block_cipher,

pyproject.toml

@@ -46,7 +46,8 @@ invest = "natcap.invest.cli:main"
 # available at runtime.
 requires = [
     'setuptools>=61', 'wheel', 'setuptools_scm>=8.0', 'cython>=3.0.0', 'babel',
-    'oldest-supported-numpy'
+    'oldest-supported-numpy; python_version<="3.8"',
+    'numpy>=2; python_version>="3.9"',  # numpy 2 only available for 3.9+
 ]
 build-backend = "setuptools.build_meta"
 

requirements.txt

@@ -13,11 +13,11 @@
 GDAL>=3.4.2
 Pyro4==4.77  # pip-only
 pandas>=1.2.1
-numpy>=1.11.0,!=1.16.0,<2.0
+numpy>=1.11.0,!=1.16.0
 Rtree>=0.8.2,!=0.9.1
 shapely>=2.0.0
 scipy>=1.9.0,!=1.12.*
-pygeoprocessing>=2.4.2  # pip-only
+pygeoprocessing>=2.4.6  # pip-only
 taskgraph>=0.11.0
 psutil>=5.6.6
 chardet>=3.0.4